Search Results for "hg19"

CrossMap is a program for convenient conversion of genome coordinates and genomeannotation files between assemblies (eg. lift from GRCh36/hg18 to GRCh37/hg19 or vice versa).It support file in BAM, SAM, BED, Wiggle, BigWig, GFF, GTF format.

Massively parallel sequencing of cDNA reverse transcribed from RNA (RNASeq) provides an accurate estimate of the quantity and composition of mRNAs. To characterize the transcriptome through the analysis of RNA-seq data, we developed PRADA. PRADA focuses on the processing and analysis of gene expression estimates, supervised and unsupervised gene fusion identification, and supervised intragenic deletion identification. PRADA currently supports 7 modules to process and identify...

... transcripts that do not overlap with any other transcripts in the gene. For example, this occurs in the ENSG00000125388 gene from ENSEMBL/hg19. We are aware of this issue and will eventually change the behavior, but for now a simple solution is just to sum the FPKMs since the gene FPKMs are just the sum of the transcript FPKMs anyways. The details on this is discussed at http://seqanswers.com/forums/showthread.php?t=5224

... sequencing data. EXCAVATOR has been published on Genome Biology (http://genomebiology.com/2013/14/10/R120/abstract). #################### ATTENTION!!!!! In order to use properly the EXCAVATOR tool, users must download the uniqueome mappability files at the following link: http://grimmond.imb.uq.edu.au/uniqueome/downloads/hg19_uniqueome.coverage.base-space.25.1.Wig.gz (for hg19) http://grimmond.imb.uq.edu.au/uniqueome/downloads/hg18_uniqueome.coverage.base-space.25.1.Wig.gz